[Open Babel] match atom order in two pdb files of same molecule

[dalvarez <alg...@gm...>]

Hi there,

I'm trying to obtain a rotation matrix between two pdb files containing the
same protein. For many of them the following script works perfectly:

# Load files in OBMol
S = next(pybel.readfile('pdb',struc))
S.removeh()
T = next(pybel.readfile('pdb',target))
T.removeh()

# Align
align = openbabel.OBAlign(False,False)
align.SetRefMol(S.OBMol)
align.SetTargetMol(T.OBMol)
if align.Align():
        OBrotMat = align.GetRotMatrix()

The problem comes when the atom order is not the same in the two files. 
As suggested in other posts, i tried:

> babel input.pdb -O output.pdb --canonical

But it results in a Segmentation Fault, or memory failure due to the large
number of atoms in the file. 
Anyone can help me working this out? What methods, classes should i use to
do this job within the script before the alignment?

Thanks in advance!

Daniel




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